Query blockers are common (I provided 2 simple examples myself), don't misquote me. Query blockers in the form provided by jaytea are not. Most are setup to specifically block certain names or message patterns beforehand. As I mentioned, these specific types of scripts would not be affected by the change.
The only ones that would be are those that arbitrarily block nicknames based on modal user input (an invalid case, as I mentioned), or flood control scripts. For flood control, there are alternatives out there (like mIRC's builtin flood control), and worst case scenario is that you accidentally trip your flood control with /query, so it's not a huge incompatibility.
Also, given how *common* query blockers are, how easy they are to script, and how many alternatives are available (server-side ignore, /ignore, mIRC flood control, etc.), breaking a few of these scripts becomes less of a big deal. At least in this case, users have alternatives, and the simplicity of these scripts (they all seem to be < 100 lines of code) means it is trivial to fix them.
Progress should not be stunted simply for backwards compatibility's sake. There's more to the argument than "scripts will break"-- part of the question is: "how bad will it be if they break?". In this case, not so bad.
